what was the command line and screen output of the binarization? And are
you saying that pre-binarization you have locations that are above
threshold, but they are set to 0 anyway?
On Thu, 28 Jan 2016, Erik Lindberg wrote:
Dear Bruce and Freesufers,
I get the following message:
surfer: Interpreting overlay
volume/media/EHD/ALLA_FREESUFER_PROCESSING_TIDIS_NOMAS_AD/qdec/lh.kvot_gender.glm
dir/Gend/thresholded.mgh as encoded scalar volume.
the two volumes I tried to convert:
1)
Volume information for sig.mgh
type: MGH
dimensions: 163842 x 1 x 1
voxel sizes: 1.0000, 1.0000, 1.0000
type: FLOAT (3)
fov: 163842.000
dof: 0
xstart: -81921.0, xend: 81921.0
ystart: -0.5, yend: 0.5
zstart: -0.5, zend: 0.5
TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00
degrees
nframes: 1
PhEncDir: UNKNOWN
ras xform present
xform info: x_r = -1.0000, y_r = 0.0000, z_r = 0.0000, c_r =
0.0000
: x_a = 0.0000, y_a = 0.0000, z_a = 1.0000, c_a =
0.0000
: x_s = 0.0000, y_s = -1.0000, z_s = 0.0000, c_s =
0.0000
talairach xfm :
Orientation : LIA
Primary Slice Direction: coronal
voxel to ras transform:
-1.0000 0.0000 0.0000 81921.0000
0.0000 0.0000 1.0000 -0.5000
0.0000 -1.0000 0.0000 0.5000
0.0000 0.0000 0.0000 1.0000
voxel-to-ras determinant -1
ras to voxel transform:
-1.0000 0.0000 0.0000 81921.0000
-0.0000 -0.0000 -1.0000 0.5000
-0.0000 1.0000 -0.0000 0.5000
0.0000 0.0000 0.0000 1.0000
2)
Volume information for cache.th13.abs.sig.cluster.mgh
type: MGH
dimensions: 163842 x 1 x 1
voxel sizes: 1.0000, 1.0000, 1.0000
type: FLOAT (3)
fov: 163842.000
dof: 0
xstart: -81921.0, xend: 81921.0
ystart: -0.5, yend: 0.5
zstart: -0.5, zend: 0.5
TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00
degrees
nframes: 1
PhEncDir: UNKNOWN
ras xform present
xform info: x_r = -1.0000, y_r = 0.0000, z_r = 0.0000, c_r =
0.0000
: x_a = 0.0000, y_a = 0.0000, z_a = 1.0000, c_a =
0.0000
: x_s = 0.0000, y_s = -1.0000, z_s = 0.0000, c_s =
0.0000
talairach xfm :
Orientation : LIA
Primary Slice Direction: coronal
voxel to ras transform:
-1.0000 0.0000 0.0000 81921.0000
0.0000 0.0000 1.0000 -0.5000
0.0000 -1.0000 0.0000 0.5000
0.0000 0.0000 0.0000 1.0000
voxel-to-ras determinant -1
ras to voxel transform:
-1.0000 0.0000 0.0000 81921.0000
-0.0000 -0.0000 -1.0000 0.5000
-0.0000 1.0000 -0.0000 0.5000
0.0000 0.0000 0.0000 1.0000
Although both these overlays have significant areas - nothing appears on the
binarized version after the conversion
Best wishes,
Olof Lindberg
Olof Lindberg PhD
Novum plan 5
NVS department section clinical geriatrics
14186 Stockholm
+46722255711
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